30PU | pdb_000030pu

Structure of a TrkB:BDNF complex

• PDB DOI: https://doi.org/10.2210/pdb30PU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2026-05-07 Released: 2026-11-04 
• Deposition Author(s): Briggs, D.C., McDonald, N.Q.
• Funding Organization(s): The Francis Crick Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

A sulfotyrosine-motif in the human TrkB extracellular domain is required for activation by the agonist antibody ZEB85

Briggs, D.C., Duffy, R., Ateaque, S., Maslen, S., Nagaraj, H., Barde, Y.A., DiStefano, P.S., Lindsay, R.M., Armstrong, P.C., Peach, C.J., McDonald, N.Q.

(2026) Pnas 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization, gel filtration, homology

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.39 kDa 
• Atom Count: 7,409 
• Modeled Residue Count: 936 
• Deposited Residue Count: 1,022 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BDNF/NT-3 growth factors receptor	A, C	392	Homo sapiens	Mutation(s): 5  Gene Names: NTRK2, TRKB EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16620 (Homo sapiens) Explore Q16620  Go to UniProtKB:  Q16620
PHAROS:  Q16620 GTEx:  ENSG00000148053
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q16620-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotrophic factor BDNF precursor form	B, D	119	Homo sapiens	Mutation(s): 0  Gene Names: BDNF
UniProt & NIH Common Fund Data Resources
Find proteins for P23560 (Homo sapiens) Explore P23560  Go to UniProtKB:  P23560
PHAROS:  P23560 GTEx:  ENSG00000176697

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth C], I [auth C], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.879	α = 90
b = 179.732	β = 90.04
c = 183.445	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Briggs, D.C., McDonald, N.Q.

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Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	CC2068

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release